The Faculty of Medicine & Surgery was formally instituted as the Collegio Medico on the 25 May 1771 as one of the faculties of the Pubblica Università di Studi Generali established a few years earlier on the 22 November 1769 decree signed by Grand Master Pinto de Fonseca, and authorised by the papal brief dated 20 October 1769. At the time of foundation of the University, the Principe dell'Accademia dei Medici was Michelangelo Grima who also held the Chair of Anatomy and Surgery.

Other members of the Accademia included Giorgio Locano, Gaetano Azzopardi, Giorgio Imbert, Gio Domenico Biagio, Giuseppe Bigeni and Lorenzo Thein. The Accademia was the body responsible for conducting the student examinations. The first statute of the new university was published on the 22 May 1771. The Medical Course lasted for five years, the student obtaining a Bachelorship after two years, a Licentiate after four years and the Doctorate after the final year. The subjects studied included botany, chemistry, anatomy, surgery and medicine. The licence to practice the profession was only given after serving six years at the Sacra Infermeria.

With the occupation of the Islands by the French in 1798, formal University teaching was abolished by General Napoleon Bonaparte by decree published on 18th June 1798. A few weeks after the French were forced to leave, Sir Alexander Ball re-instituted the University on 6th November 1800 and medical studies were resumed that same year with the first three doctors qualifying in 1804. During the first two decades of the nineteenth century, only a licentiate was granted to successful candidates. The doctorate was introduced in 1822, this being granted a year after the end of studies. The licentiate was abolished in 1838 after the publication of the 1838 Fundamental Statute of the University of Malta which brought the medical faculty into line with medical schools in England.

The Faculty of Medicine & Surgery has strived throughout the decades of the later 19th and 20th century to keep in touch with the changes occurring in medical education on the European arena, particularly with those occurring in the United Kingdom. In 1898-99 permission was granted to medical graduates from Malta to sit for the final examination of the Conjoint Board of the Royal College of Physicians and the Royal College of Surgeons, and for the diploma of the Society of Apothecaries of London.

In 1901 the Medical Degree of the Malta University obtained official recognition throughout the British Empire and entitled graduates to be registered in England as Colonial Practitioners. This recognition enabled Maltese graduates to seek their professional fortunes overseas throughout the Commonwealth and to continue their medical education in the various developing specialities. Other individuals sought their career progression on the European mainland. The entry of Malta into the European Union continues to ensure that the Maltese medical qualification enjoys recognition by all member states.